[root@7b2785c8d5cb 15:50:43 /work/my_pop_cucu/01.phylo_tree]# run_pipeline.pl -Xmx5G -importGuess $workdir/00.filter/clean.vcf.gz \
> -ExportPlugin -saveAs supergene.phy -format Phylip_Inter
/biosoft/tassel5/lib/javax.json-1.0.4.jar:/biosoft/tassel5/lib/colt-1.2.0.jar:/biosoft/tassel5/lib/jcommon-1.0.23.jar:/biosoft/tassel5/lib/trove-3.0.3.jar:/biosoft/tassel5/lib/itextpdf-5.1.0.jar:/biosoft/tassel5/lib/ahocorasick-0.2.4.jar:/biosoft/tassel5/lib/biojava-alignment-4.0.0.jar:/biosoft/tassel5/lib/junit-4.10.jar:/biosoft/tassel5/lib/phg.jar:/biosoft/tassel5/lib/kotlin-stdlib-1.3.50.jar:/biosoft/tassel5/lib/htsjdk-2.19.0.jar:/biosoft/tassel5/lib/sqlite-jdbc-3.8.5-pre1.jar:/biosoft/tassel5/lib/slf4j-simple-1.7.10.jar:/biosoft/tassel5/lib/json-simple-1.1.1.jar:/biosoft/tassel5/lib/ejml-0.23.jar:/biosoft/tassel5/lib/jfreesvg-3.2.jar:/biosoft/tassel5/lib/forester-1.038.jar:/biosoft/tassel5/lib/mail-1.4.jar:/biosoft/tassel5/lib/fastutil-8.2.2.jar:/biosoft/tassel5/lib/commons-codec-1.10.jar:/biosoft/tassel5/lib/snappy-java-1.1.1.6.jar:/biosoft/tassel5/lib/jhdf5-14.12.5.jar:/biosoft/tassel5/lib/postgresql-9.4-1201.jdbc41.jar:/biosoft/tassel5/lib/slf4j-api-1.7.10.jar:/biosoft/tassel5/lib/gs-ui-1.3.jar:/biosoft/tassel5/lib/guava-22.0.jar:/biosoft/tassel5/lib/commons-math3-3.4.1.jar:/biosoft/tassel5/lib/jfreechart-1.0.19.jar:/biosoft/tassel5/lib/gs-core-1.3.jar:/biosoft/tassel5/lib/biojava-core-4.0.0.jar:/biosoft/tassel5/lib/kotlinx-coroutines-core-1.3.0.jar:/biosoft/tassel5/lib/biojava-phylo-4.0.0.jar:/biosoft/tassel5/lib/scala-library-2.10.1.jar:/biosoft/tassel5/lib/log4j-1.2.13.jar:/biosoft/tassel5/lib/sTASSEL.jar:/biosoft/tassel5/sTASSEL.jar
Memory Settings: -Xms512m -Xmx5G
Tassel Pipeline Arguments: -importGuess /work/my_pop_cucu/00.filter/clean.vcf.gz -ExportPlugin -saveAs supergene.phy -format Phylip_Inter
[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.64 Date: July 9, 2020
[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 4949 MB
[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_302
[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Linux
[main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 1
[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -importGuess, /work/my_pop_cucu/00.filter/clean.vcf.gz, -ExportPlugin, -saveAs, supergene.phy, -format, Phylip_Inter, -runfork1]
net.maizegenetics.analysis.data.FileLoadPlugin
net.maizegenetics.analysis.data.ExportPlugin
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.FileLoadPlugin: time: Oct 30, 2023 15:54:45
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
FileLoadPlugin Parameters
format: Make Best Guess
sortPositions: false
keepDepth: true
[pool-1-thread-1] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Start Loading File: /work/my_pop_cucu/00.filter/clean.vcf.gz time: Oct 30, 2023 15:54:45
[pool-1-thread-1] INFO net.maizegenetics.analysis.data.FileLoadPlugin - guessAtUnknowns: type: VCF
[root@7b2785c8d5cb 15:55:05 /work/my_pop_cucu/01.phylo_tree]# ll
total 0
-rwxr-xr-x 1 root root 0 Oct 30 15:10 fasttree.nwk
-rwxr-xr-x 1 root root 591 Oct 30 15:09 iqtree.log
[root@7b2785c8d5cb 16:01:28 /work/my_pop_cucu/01.phylo_tree]#
